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Next Generation Sequencing and Its Application in Livestock

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Next Generation Sequencing and Its Application in Livestock Journal of Entomology and Zoology Studies 2018; 6(3): 1601-1609 E-ISSN: 2320-7078 P-ISSN: 2349-6800 Next generation sequencing and its application in JEZS 2018; 6(3): 1601-1609 © 2018 JEZS livestock Received: 18-03-2018 Accepted: 23-04-2018 Vandana Yadav Vandana Yadav, BL Saini, Narendra Pratap Singh, Neeti Lakhani and Ph.D. Scholar, Animal Genetics, Rahul Sharma ICAR-NDRI, ICAR-National Dairy Research Institute, Karnal, Haryana, India Abstract The ability to determine nucleic acid sequences is one of the most important platforms for the detailed BL Saini study of biological systems. Next generation sequencing (NGS) technology has revolutionized genomic Ph.D Scholar, Animal Genetics, and genetic research. Starting from the basic Sanger sequencing, the next generation sequencing are ICAR-IVRI, ICAR-National providing high throughput and much cheaper alternative. All NGS have a similar base methodology that Dairy Research Institute, includes template preparation, sequencing and imaging, and data analysis. Different NGS platform use Karnal, Haryana, India different technology for the identification of the called base. Different commercially available technologies include 454 FLX Roche (pyrosequecing), Illumina Solexa (CRT), ABI SOLiD (sequencing Narendra Pratap Singh M.V.Sc Scholar, Animal genetics, by ligation) and Ion semiconductor sequencing (Ion Torrent) which require the pre-amplification process ICAR- NDRI, ICAR-National before sequencing. Single molecule approach are the developing technology for sequencing which can Dairy Research Institute, provide the @1000$ per genome. Single molecule technology includes Helicos sequencer, SMRT, Karnal, Haryana, India Nanopore technology that does not require the amplification prior to sequencing. Data analysis can be time-consuming and may require special knowledge of bioinformatics to gather accurate information Neeti Lakhani from sequence data. Resequencing of the human genome is being performed to identify genes and Ph.D Scholar, Nutrition division, regulatory elements involved in pathological processes. NGS has also provided a wealth of knowledge ICAR-NDRI, ICAR-National for comparative biology studies through whole genome sequencing of a wide variety of organisms. Dairy Research Institute, Simply analyzing all DNA from control versus infected (diseased) individuals will reveal the “extra” Karnal, Haryana, India DNA, which most likely derives from the infectious agent. The approach was used successfully to identify e.g. colony collapse disorder killing honeybees but also to identify the cause of diseases that Rahul Sharma killed thousands of humans in the past. Thus NGS can be used for genomics, trancriptomics, epigenetic VEO, DAH, Katni, Madhya study and metagenomics study. Pradesh, India Keywords: Sanger sequencing, nucleotide bases, template, adapter 1. Introduction DNA sequencing is the process of determining the precise order of nucleotide bases (adenine, guanine, cytosine, and thymine) within a DNA molecule. The advancement in DNA sequencing technology has been proved to be a boon for biological and medical research and discovery. Knowledge of DNA sequences is not only required for basic biological research but in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematic. The modern DNA sequencing technology with rapid speed has been instrumental in the sequencing of the complete DNA sequences, or genomes of numerous types and various life forms, including the human genome and other complete DNA sequences of many animal, plants, and microbial species. 2. History of sequencing Ray Wu at Cornell University (1970) established the first method for determining DNA sequences, based on a location-specific primer extension strategy. The cohesive ends of lambda phage DNA were sequenced by using DNA polymerase catalysis and specific nucleotide labeling, both of which forms the base for the current sequencing technologies [1]. This primer-extension strategy was then used to develop more rapid DNA sequencing Correspondence Vandana Yadav methods. Frederick Sanger (1977) at the MRC Centre, Cambridge, UK then developed the Ph.D. Scholar, Animal Genetics, method for "DNA sequencing with chain-terminating inhibitors". In the same year Walter ICAR-NDRI, ICAR-National Gilbert and Allan Maxam at Harvard also developed another method for DNA sequencing Dairy Research Institute, known as “DNA sequencing by chemical degradation”. In 1987, Applied Biosystems gave the Karnal, Haryana, India first full-automated sequencer (ABI370) for the first time. ~ 1601 ~ Journal of Entomology and Zoology Studies After that various high throughput-sequencing platforms 3. Next-generation sequencing methods (Pyrosequencing-2005, Illumina-2006, Ion torrent-2011, Pac- Generation refers to the chemistry and technology used by the Bio- 2012, illumine HiseqX-2013, Nanopore- 2014) were sequencing process. First generation generally refers to launched, marking the era of sequencing. The advancement in Sanger sequencing. "Next-generation" is generally used to sequencing technologies has now made it possible to refer to any of the high-throughput methods which were sequence the complete genome within a short time and in a developed after Sanger. Third-generation refers to single- cost effective manner. molecule methods (Helicos and Pac-Bio SMRT) and fourth generation includes the Nano-pore sequencing (Fig: 1). Fig 1: Different NGS platforms 3.1 Sanger method of sequencing invented by Frederick Sanger in 1977 & got Nobel Prize in It was the most common approach used for DNA sequencing 1980. Fig 2: Sanger sequencing by chain termination This method is also termed as Chain Termination or Dideoxy polymerase, a short primer DNA to enable the polymerase to method (Fig: 2). It relies on the use of dideoxyribonucleoside start DNA synthesis, and the four deoxyribonucleoside triphosphate, derivative of the normal deoxyribonucleoside triphosphate (dATP, dCTP, dGTP, dTTP) [3]. If a triphosphate that lack the 3′ hydroxyl group [2]. It is based on dideoxyribonucleotide analog of one of these nucleotides is the synthesis of DNA in a controlled way to generate also present in the mixture, it can incorporate into a growing fragments terminating at specific point. Purified DNA is DNA chain. Because this chain now lacks a 3′ OH group, the synthesized in vitro in a mixture that contains single stranded addition of next nucleotide is blocked, and the DNA chain molecules of the DNA to be sequenced, the enzyme DNA terminates at that point. ~ 1602 ~ Journal of Entomology and Zoology Studies To determine the complete sequence of a DNA fragment, the dramatic increase in cost-effective sequence throughput, double- stranded DNA is first separated into its single strands albeit at the expense of read lengths [5]. The next-generation and one of the strands is used as a template for sequencing. technologies commercially available today include the 454 Four different chain- terminating dideoxyribonucleoside GS20 pyrosequencing based instrument (Roche Applied triphosphates (ddATP, ddCTP, ddGTP, ddTTP) are used in Science), the Solexa 1G analyzer (Illumina, Inc.), the SOLiD four separate DNA synthesis reactions on copies of the same instrument from Applied Biosystems, and the Heliscope from single-stranded DNA template. Each reaction produces a set Helicos, Inc. and Nanopore from Oxford [6]. of DNA copies that terminate at different points in the sequence. The products of these four reactions are separated 5. Workflow of next-generation sequence by electrophoresis in four parallel lanes of a thin slab The workflow to produce next-generation sequence-ready polyacrylamide gel. The newly synthesized fragments are libraries is straightforward and includes sample preparation, detected by a label (either radioactive or fluorescent) that has library construction, clonal amplification, sequencing and data been incorporated either into the primer or into of the analysis (Fig: 3). deoxyribonucleoside triphosphates used to extend the DNA chain [4]. In each lane, the bands represent fragments that have a. Sample preparation been terminated at a given nucleotide but at different Source of sample (DNA, RNA) positions in the DNA. By reading off the bands in order, Qualify and quantify samples starting at the bottom of the gel and working across all lanes, the DNA sequence of the newly synthesized strands can be b. Library Construction determined. Thus, a long and labor-intensive process was Prepare platform specific library. completed, and the sequencing data for the DNA of interest Fragmentation of target DNA and adapter ligation. were in hand and ready for assembly, translation to amino acid sequence, or other types of analysis. c. Clonal Amplification Bridge PCR amplification-Illumina sequencing. 4. Advances in DNA sequencing technologies Emulsion PCR-SOLiD, Ion torrent and pyrosequencig. The landmark publications of the late 1970 s by Sanger's and Third and fourth generation sequencing technologies Gilbert's groups and notably the development of the chain don’t require amplification. termination method by Sanger and colleagues established the groundwork for decades of sequence-driven research that d. Sequencing followed. The chain-termination method published in 1977 Perform sequencing run reaction on NGS platform. also commonly referred to as Sanger or dideoxy sequencing, Sequencing by ligation-SOLiD sequencing. has remained the most commonly used DNA sequencing technique to date and was
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